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  <front>
    <journal-meta />
    <article-meta>
      <title-group>
        <article-title>Identifying Used Methods and Datasets in Scientific Publications</article-title>
      </title-group>
      <contrib-group>
        <contrib contrib-type="author">
          <string-name>Michael F a¨rber</string-name>
          <xref ref-type="aff" rid="aff0">0</xref>
        </contrib>
        <contrib contrib-type="author">
          <string-name>Alexander Albers</string-name>
          <xref ref-type="aff" rid="aff0">0</xref>
        </contrib>
        <contrib contrib-type="author">
          <string-name>Felix Schu¨ ber</string-name>
          <xref ref-type="aff" rid="aff0">0</xref>
        </contrib>
        <aff id="aff0">
          <label>0</label>
          <institution>Karlsruhe Institute of Technology (KIT)</institution>
          ,
          <country country="DE">Germany</country>
        </aff>
      </contrib-group>
      <abstract>
        <p>Although it has become common to assess publications and researchers by means of their citation count (e.g., using the h-index), measuring the impact of scientific methods and datasets (e.g., using an h-index for datasets) has been performed only to a limited extent. This is not surprising because the usage information of methods and datasets is typically not explicitly provided by the authors, but hidden in a publication's text. In this paper, we propose an approach to identifying methods and datasets in texts that have actually been used by the authors. Our approach first recognizes datasets and methods in the text by means of a domain-specific named entity recognition method with minimal human interaction. It then classifies these mentions into used vs. non-used based on the textual contexts. The obtained labels are aggregated on the document level and integrated into the Microsoft Academic Knowledge Graph modeling publications' metadata. In experiments based on the Microsoft Academic Graph, we show that both method and dataset mentions can be identified and correctly classified with respect to their usage to a high degree. Overall, our approach facilitates method and dataset recommendation, enhanced paper recommendation, and scientific impact quantification. It can be extended in such a way that it can identify mentions of any entity type (e.g., task).</p>
      </abstract>
    </article-meta>
  </front>
  <body>
    <sec id="sec-1">
      <title>1 Introduction</title>
      <p>In the past, a huge variety of scientific methods and datasets
has been proposed in the different scientific disciplines. For
instance, Wikipedia lists several hundred datasets for the
area of machine learning.1 It is therefore unsurprising that
researchers are often unaware of which scientific methods or
data sets have already been used for a given research topic.
Furthermore, in digital libraries, such information regarding
usage of scientific methods and datasets can be very useful.
For instance, this information allows us to measure the
impact of publications and researchers in novel ways (e.g.,
hindex for datasets). In this way, authors providing methods
and datasets can be awarded properly in the light of FAIR
data principles and open research efforts.</p>
      <p>Copyright © 2021for this paper by its authors. Use permitted under
Creative Commons License Attribution 4.0 International (CC BY
4.0).</p>
      <p>1https://en.wikipedia.org/wiki/List of datasets for
machinelearning research.</p>
      <p>
        The usage of methods and datasets is typically not given
explicitly, but mentioned in publications’ full texts.
Identifying scientific methods and datasets in texts can be considered
as domain-specific named entity recognition. In the
scholarly domain, a few approaches have been proposed for
identifying concepts such as datasets
        <xref ref-type="bibr" rid="ref10 ref11 ref14 ref18">(Mesbah et al. 2018; Luan
2019; Luan et al. 2018; Tsai, Kundu, and Roth 2013)</xref>
        . For
instance, Tsai, Kundu, and Roth (2013) propose a method
to extract concepts from scientific publications. They limit
their extraction method to entities that are followed by a
citation indicator and only extract all mentioned concepts, rather
than ones explicitly used.
        <xref ref-type="bibr" rid="ref3">Ga´bor et al. (2018)</xref>
        , in contrast,
proposed a method to classify entity mentions into used and
non-used. However, usage relations are only considered
between entities of a specific type and not with respect to
the papers’ authors. Overall, a state-of-the-art approach that
can recognize and classify scientific methods and datasets
is, to the best of our knowledge, missing so far. Moreover,
no large data set has been published that allows tasks for
method/dataset-centric scientific impact quantification.
      </p>
      <p>In this paper, we develop a framework to recognize
entities of type DATASET and METHOD in scientific
publications, as well as to classify them as used vs. non-used.
Our framework consists of a domain-specific named entity
recognition step, a classification step for determining the
actual usage, and an aggregation step for retrieving the used
methods and datasets on the document level. Our approach
is designed to extract information about entities from
scientific publications in an automated way, requiring
minimal human interaction. We provide the usage information
of about 771,000 methods and 449,000 datasets online for
further usage. Moreover, we integrate the information into
the Microsoft Academic Knowledge Graph (MAKG), which
models information of more than 120 million scientific
publications, and thereby provides the basis for scientific impact
quantification studies (e.g., designing “h-index”-like metrics
for scientific methods and datasets).</p>
      <p>
        Overall, the main contributions of this paper are as
follows:
• We develop a named entity recognition approach that
extracts scientific methods and datasets from texts. Our
approach extends preliminary works
        <xref ref-type="bibr" rid="ref14">(Mesbah et al. 2018)</xref>
        by using state-of-the-art embedding techniques.
• We develop novel approaches to identify in texts the
methods and datasets authors have indeed used in their papers.
• We create an evaluation dataset of 1,000 sentences with
annotated methods and datasets and provide it to the
public.
• We perform extensive experiments and identify the best
classification method for the proposed task.
• We analyze the results of applying our framework to
computer science papers.
• We extend the MAKG with the usage information
concerning methods and datasets mentioned in 510,027
papers and provide it to the public.
      </p>
      <p>Our data and code are publicly available at https://github.
com/michaelfaerber/scholarly-entity-usage-detection.</p>
      <p>The rest of our paper is structured as follows: In Section 2,
we outline related work concerning domain-specific named
entity recognition and usage classification. In Section 3, we
describe our methods for named entity recognition and
usage classification. We present our evaluation in Section 4
and our generated dataset in Section 5, before summarizing
our findings in Section 6.</p>
      <p>2</p>
    </sec>
    <sec id="sec-2">
      <title>Related Work</title>
      <p>In the following paragraphs, we outline the most relevant
works concerning named entity recognition for long-tail
entities and the extraction of aspects of entities.</p>
      <sec id="sec-2-1">
        <title>Named Entity Recognition for Long-Tail Entities.</title>
        <p>
          In general, existing named entity recognition (NER)
approaches are of diverse nature: They utilize gazetteers,
rules, parts-of-speech tagging, dependency trees, or machine
learning techniques. State-of-the-art NER approaches are
often based on long short-term memory networks (LSTMs)
(Mysore et al. 2017), conditional random fields (CRFs)
          <xref ref-type="bibr" rid="ref14 ref19">(Mesbah et al. 2018; Vliegenthart et al. 2019)</xref>
          , or a
combination of both
          <xref ref-type="bibr" rid="ref10 ref13 ref5 ref8">(Lample et al. 2016; Ma and Hovy 2016;
Luan 2019; Jain et al. 2020)</xref>
          . Although many approaches
to named entity recognition exist, most of them require a
considerable amount of human interaction for the creation
of sufficient training data. Few classification approaches
take into consideration that most of the considered entities
are long-tail entities (i.e., appearing infrequently in
documents and often not represented in public knowledge
repositories, such as Wikidata). To reduce the required amount
of human-labeled training data, iterative and active
learning techniques have been proposed, particularly for
scientific publications
          <xref ref-type="bibr" rid="ref11 ref14 ref17 ref19">(Tchoua et al. 2019; Mesbah et al. 2018;
Vliegenthart et al. 2019; Luan et al. 2018)</xref>
          .
          <xref ref-type="bibr" rid="ref14">Mesbah et al.
(2018)</xref>
          , for instance, introduce TSE-NER, which iteratively
expands a predefined seed set of terms without additional
human input. The authors apply several heuristic filtering
methods to automatically create positive and negative
classification examples. Our approach to named entity
recognition is based on TSE-NER, but extends it by using SciBERT
embeddings.
          <xref ref-type="bibr" rid="ref19">Vliegenthart et al. (2019)</xref>
          also extend the
TSENER approach by relying on human feedback for newly
added labels. Although the authors achieve a lower rate of
added false positives, this semi-supervised technique
reintroduces the need for human labor and thus does not meet
our requirements.
          <xref ref-type="bibr" rid="ref17">Tchoua et al. (2019)</xref>
          present a dedicated
NER approach for material sciences to recognize polymer
names. The approach is based on active learning to
overcome the data sparsity problem.
          <xref ref-type="bibr" rid="ref11">Luan et al. (2018)</xref>
          introduce a multi-task setup of identifying entities, relations, and
coreference clusters in scientific articles. Although the
approach is valuable in settings where not only named entities
but facts need to be extracted from text, the authors do not
specifically consider the usage of datasets and methods by
the papers’ authors.
        </p>
      </sec>
      <sec id="sec-2-2">
        <title>Identifying Aspects of Entities. Apart from recognizing</title>
        <p>
          named entities, a few approaches take additional aspects of
the entities, such as the actual usage of entities, into account.
          <xref ref-type="bibr" rid="ref4">Gupta and Manning (2011)</xref>
          introduce a method to identify
the focus, domain of application, and technique from
computational linguistics papers, but this approach only extracts
broad topics.
          <xref ref-type="bibr" rid="ref5">Jain et al. (2020)</xref>
          focus on detecting and
extracting salient information from publications. They define
salient information as information (e.g., named entities) that
are needed to describe the results of an article. In contrast,
our goal is to find all used entities to gain enhanced insight
into the general usage of methods and datasets.
        </p>
        <p>3</p>
      </sec>
    </sec>
    <sec id="sec-3">
      <title>Approach</title>
      <p>Our framework for identifying methods and datasets authors
use in a given text document is depicted in Figure 1. We can
differentiate between the following steps:
1. We build a named entity recognition model to extract
named entities of a given scientific paper.
2. We perform a classification of each named entity into used
and non-used (i.e., merely mentioned) on a sentence level.
3. We aggregate the sentence-level classifications of all
named entities in a document.</p>
      <p>The obtained list of methods and datasets used per
document can be further analyzed in various ways. For a neat
alignment with papers’ metadata, we extend the Microsoft
Academic Knowledge Graph (MAKG) with this new data.
In this way, metadata of publications, authors, venues, and
research areas can be used for advanced scholarly data
mining (e.g., for novel ways of research impact assessment).</p>
      <p>In the following, we present the single steps of our
pipeline in more detail.
3.1</p>
      <sec id="sec-3-1">
        <title>Named Entity Recognition</title>
        <p>
          For named entity recognition, we adapt the TSE-NER
          <xref ref-type="bibr" rid="ref14">(Mesbah et al. 2018)</xref>
          to our needs. TSE-NER is based on the
hypothesis that entities of the same type are mostly used in
a similar context. For example, objects of the entity type
DATASET may be mentioned in the documents via phrases
such as “we used data set X” or “we could achieve a recall
of 0.4 on data set Y.” Identifying such patterns automatically
in the text allows us to identify additional, unknown
entities in the text – particularly long-tail entities. The contexts
of these newly found entity mentions can then be mined in
another iteration, leading to additional patterns for named
entity recognition.
        </p>
        <p>
          An in-depth introduction to the original TSE-NER
approach is provided by
          <xref ref-type="bibr" rid="ref14">Mesbah et al. (2018)</xref>
          . In the
following, we outline the main steps of our named entity
recognition approach and the main differences from the original
TSE-NER approach.
1. We start with an initial set of METHOD and DATASET
instances as seed terms (e.g., “SVM” and “MNIST”). These
seed terms can, for instance, be gathered from existing
knowledge graphs. In contrast to the original approach of
Mesbah et al., we consider all computer science methods
and datasets. The seed term selection is explained in
Section 4.
2. We expand the list of seed terms by applying term
and sentence expansion (TSE). In contrast to the
original method, we use SciBERT as a semantic relatedness
method and cluster the new entities using k-means.
3. Using the expanded set of entities, we annotate named
entities in the training data. As context for each named entity
we consider the current sentence as well as the preceding
and subsequent sentence.
4. Using the annotated training set, we apply our NER
approach and thereby identify new entity candidates. We use
a CRF algorithm to learn the patterns of the data.
5. Finally, we filter the entity candidates to prevent
misclassification and ensure data quality. We start with simple
parts-of-speech analysis and stop-word removal methods
to keep relevant nouns. Then, we use knowledge graph
information and similarity scores to remove those entities
with low similarity and no reference.
        </p>
        <p>The output of our named entity recognition approach is a
list of mentioned scientific methods and datasets with their
positions in the texts.</p>
      </sec>
      <sec id="sec-3-2">
        <title>Usage Classification</title>
        <p>In total, we present four approaches for detecting used
entity mentions of type METHOD or DATASET. For each model,
we first apply an embedding-based method to transform the
texts into a feature space, and then apply a classification
algorithm to classify usage. In the following, we outline our
approaches.</p>
      </sec>
      <sec id="sec-3-3">
        <title>Model 1: TF-IDF + Random Forest As a baseline model,</title>
        <p>we use term frequency-inverse document frequency (tf-idf)
to represent the words of a text as vectors. Based on
preliminary evaluations of several standard classification methods,
we choose a random forest classifier for classification into
used and non-used.</p>
        <p>
          Model 2: SciBERT + Random Forest For our second
model, we make use of SciBERT
          <xref ref-type="bibr" rid="ref1">(Beltagy, Lo, and Cohan
2019)</xref>
          , a BERT-based language model pretrained on
scientific publications. This embedding model has been used for
various tasks, such as scientific text classification and
recommendation. In our use case, we use SciBERT embeddings
to create feature vectors and a random forest classifier for the
binary classification.
        </p>
      </sec>
      <sec id="sec-3-4">
        <title>Model 3: SciBERT + SciBERT Our third model is based</title>
        <p>
          on a fine-tuned SciBERT model for sequence classification.
Beltagy, Lo, and Cohan (2019) show that fine-tuning
SciBERT clearly improves the classification score, especially in
the field of computer science. Hence, in comparison to the
second model, we now also use SciBERT to make the
classification by fine-tuning it to our annotated data. For the
classification task, SciBERT uses a linear classification layer.
Model 4: SciBERT + CNN Our fourth model uses
SciBERT embeddings as feature vectors and a convolutional
neural network (CNN) for the classification task. Using the
CNN approach as introduced by
          <xref ref-type="bibr" rid="ref7">Kim (2014)</xref>
          as an advanced
classification technique aims to capture the complex
structures of word embeddings, which should result in a more
accurate classification score.
The method described above allows us to make a
prediction for each occurrence of a named entity (i.e., entity-level
prediction). To predict at the document level whether each
unique named entity of a document is used or only
mentioned or proposed, we aggregate all entity-level predictions
to a document level prediction using majority vote.
We use our results to extend the MAKG
          <xref ref-type="bibr" rid="ref2">(Fa¨rber 2019)</xref>
          ,
which models publications’ metadata for all scientific
disciplines. Given that the MAKG is provided in the Resource
Description Framework (RDF), we introduce the property
:used methods, which associates a paper with a used
method. Because no knowledge graph contains all of the
extracted methods and datasets, we refrain from linking to
URIs in other knowledge graphs.
        </p>
        <p>4</p>
      </sec>
    </sec>
    <sec id="sec-4">
      <title>Evaluation</title>
      <p>In the following, we outline our evaluations of all three steps
of our pipeline. First, we compare the results of our
modified TSE-NER model to the original paper. Next, we
evaluate our usage classification models on our annotated test
data. Finally, we apply our pipeline to full-text papers from
the computer science domain to analyze trends over time in
various computer science fields.
4.1</p>
      <sec id="sec-4-1">
        <title>Named Entity Recognition</title>
        <p>
          Evaluation Settings
(1) Training. We train our named entity recognition model
on all 7 million abstracts of computer science papers given in
the Microsoft Academic Graph (MAG; v2019-12-26)
          <xref ref-type="bibr" rid="ref16">(Sinha
et al. 2015)</xref>
          . For the methods, we use the same 50 seed sets
as the authors of the original paper. For DATASETS, we
create our own set of seed terms because we were only able to
expand very few sentences from our corpus using the
original terms.2 For our initial assessment, we run two iterations
for each entity type, which according to the authors should
already yield good results with a high precision value.
Running more than two iterations increases recall at the cost
of precision due to the addition of too many unrelated seed
terms.
        </p>
        <p>
          (2) Testing. To evaluate the NER approach, we use the
SciREX dataset
          <xref ref-type="bibr" rid="ref5">(Jain et al. 2020)</xref>
          , which includes
annotations of full-text papers from the machine learning domain
for the METHOD and DATASET entity types. In this way, we
can reuse existing evaluation data sets and compare our
evaluation results with the evaluation results of the original
TSENER
          <xref ref-type="bibr" rid="ref14">(Mesbah et al. 2018)</xref>
          . Although the authors of
TSENER only apply their evaluation to triples consisting of a
2We extract 73 data set names from Wikipedia
(https://en.wikipedia.org/wiki/List of datasets for
machinelearning research) and Wikidata (https://w.wiki/RrU) based on our
knowledge in the machine learning domain.
        </p>
        <p>
          R
sentence containing the test entity, as well as the preceding
and the succeeding sentence
          <xref ref-type="bibr" rid="ref14">(Mesbah et al. 2018)</xref>
          , we apply
our model to full-text documents, which we regard as a more
realistic setting.
        </p>
        <p>As in the original paper, we calculate precision, recall,
and F1 scores for the named entity recognition of METHOD
and DATASET instances. We count partial matches as correct
predictions because in most cases we do not need to cover
the full span of an entity to gain meaningful insight.
Evaluation Results
(1) Study on Embeddings. The original TSE-NER
approach is based on word2vec embeddings. Thus, we first
analyze the difference in performance when using SciBERT
token embeddings instead of word2vec embeddings for term
clustering and similar terms filtering (see the steps 2 and 5
in Sec. 3.1) influences the clustering performance. We
qualitatively study the clustering results of the term expansion
in the first iteration for the METHOD type and find that, in
general, both approaches generate very consistent clusters
that differ based on various computer science fields. Given
that the word2vec model had to be trained from scratch, it
achieves surprisingly good results. Nevertheless, clustering
based on SciBERT embeddings yields far more and richer
terms, because it is not limited to just bigrams. Single
clusters contain more variations of the same terms and
generally contain better results. One risk of using SciBERT is
that terms, such as Netflix or GitHub, are clustered together
with dataset names, which is likely caused by both terms
being used in the context of datasets but not being recognized
jointly with neighboring terms. This may decrease the NER
performance if names of other unrelated organizations are
added as a result in the following iterations.</p>
        <p>
          (2) NER Evaluation Results.
          <xref ref-type="bibr" rid="ref14">Mesbah et al. (2018)</xref>
          achieve precision and recall values of 0.79 and 0.24 for the
METHOD type and 0.83 and 0.10 for the DATASET type. The
authors’ TSE-NER model was trained based on 100 initial
seed terms and the same sentence expansion and filtering
strategies as our model. As shown in Table 1, we are not
able to achieve a similar high precision value as the authors
of the original paper, who used around 15,000 full-text
papers as their corpus. The obvious reason is that publications’
abstracts, as used by us, may be publicly available to a large
extent and therefore may be a good data source, but seem
to contain method and dataset names only to a limited
degree. To improve the performance of TSE-NER, we choose
to replicate a more similar corpus by using 25,060 full-text
papers instead of 7 million abstracts from the MAG, as well
as narrowing the domain to include only machine learning
papers. Although we see equal or higher recall values, this
corpus does not improve the F1 scores significantly or, in the
case of data sets, it even reduces the metric.
        </p>
        <p>Figure 2 and Figure 3 illustrate the named entity
recognition for two exemplary sections from the SciREX data set.
We can observe that, in general, the approach produces
decent results. The approach sometimes fails to capture the
complete span of an entity mention (e.g., the first word in
character embedding layer). Some of the false positive
predictions are not too far fetched, such as vector space, but
others, such as query, answer, and context, are less similar
to names of methods. This indicates that there is still a
potential to introduce better filtering strategies. One recurring
problem for the DATASET model is that the term dataset is
recognized without any specific names in its context.</p>
        <p>
          To further compare our results with the TSE-NER
publication
          <xref ref-type="bibr" rid="ref14">(Mesbah et al. 2018)</xref>
          , Table 2 shows the number of
methods and datasets collected in each step based on the
corpus containing papers’ abstracts. While the original
TSENER model used nearly 30,000 method names, our model is
only able to use 3,403 method names as training data of the
CRF. Training on the full-text corpus yields 8,355 named
entities for training. This leads to more than 90,000 extracted
named entities after the CRF training, compared to 7,469
named entities when training on abstracts, but still does not
achieve the same results as
          <xref ref-type="bibr" rid="ref14">Mesbah et al. (2018)</xref>
          . One
obvious reason for that may be that neither of our training
corpora contain as many seed entities, which results in fewer
found terms and sentences. Another reason may be that the
found sentences contain fewer similar neighboring terms
(e.g., fewer enumerations of method names or datasets),
which would result in smaller cluster sizes and thus fewer
added terms.
        </p>
        <p>
          Despite the inferior evaluation results for our
domainspecific named entity recognition of methods and datasets,
we nevertheless believe they are sufficient for the
subsequent knowledge graph expansion and trend analysis.
Because we aggregate all found entities on the document level,
we assume that a few missing mentions of the same entity
would not affect the outcome significantly. For the
subsequent tasks, we use the NER model trained on abstracts
instead of full text, because we favor higher precision over
recall for the knowledge graph extension.
4.2
We needed to create a new dataset for training and
evaluating our usage classification models. To this end, two
authors (computer scientists) manually annotated 1,000
sentences concerning the usage of mentioned method and data
sets (500 per entity type and person; see Table 4 for more
statistics). We reuse a subset of the SciREX data set
          <xref ref-type="bibr" rid="ref5">(Jain
et al. 2020)</xref>
          , which already contains annotated entities for
the METHOD and DATASET type, and manually annotate
whether an entity has been used in the given sentence and
context. To reduce training bias, we also drop duplicate
en
        </p>
        <p>R
tities. We only annotated an entity as used if it is obvious
from reading the sentence containing the entity and its
surrounding context. In any uncertain cases, we annotate the
entity as non-used. This way, we aim to achieve high
precision on the sentence level while still being able to decide
for an entity on the document level using our entity
aggregation step whether the entity has been used. We also label
an entity as used if it has been used in a comparison of
multiple approaches (i.e. as a baseline). In this way, we allow a
thorough tracking of used methods and datasets, facilitating
scientific impact quantification.</p>
        <p>To ensure high data quality and consistency of our
annotated data, we select 100 entities of the METHOD and
DATASET type that were annotated to calculate the
interannotator agreement. We achieve a satisfactory score of
0.86 for methods and 0.91 for datasets.</p>
        <p>Finally, we drop invalid entity types (e.g., entities from
SciREX that are classified as material type but do not make
sense as a data set type) and create a training and test set.
Using the same amount of used and non-used entities, we
have 802 entries for the METHOD type and 492 entries for
the DATASET type. For the evaluation, we split the annotated
data into training and test sets with a ratio of three to one.</p>
      </sec>
      <sec id="sec-4-2">
        <title>Evaluation Settings</title>
        <p>Because our usage classification task constitutes a binary
classification problem, we evaluate our models using
precision, recall, and F1 score. As outlined in Section 3.2, we
evaluate four models: (1) random forest with TF-IDF
representations, (2) random forest with SciBERT embeddings,
(3) a SciBERT classification model with SciBERT
embeddings, and (4) a CNN model with SciBERT embeddings for
text representation.</p>
      </sec>
      <sec id="sec-4-3">
        <title>Evaluation Results</title>
        <p>Comparison of Methods. Table 3 shows the evaluation
results concerning the usage classification of method and
dataset occurrences. For METHOD entities, the fine-tuned
SciBERT model performs better with only a single sentence
as input and achieves the best recall. The combined
SciBERT and CNN model works best when the preceding and
succeeding sentences are available as context. It achieves a
similar high recall and slightly better precision than the
finetuned SciBERT model.</p>
        <p>For DATASET entities, both the fine-tuned SciBERT
model and the CNN model achieve higher recall than they
do for classifying METHOD entities. SciBERT still achieves
relatively high precision scores but works better when
neighboring sentences are available. For the CNN model,
precision scores are significantly lower than they are for method
entities.</p>
        <p>Neither random forest model manages to compete with
the more sophisticated models, but work slightly better on
the DATASET entity type. Using the SciBERT sentence
embeddings instead of tf-idf consistently results in a
significantly higher precision at a cost of slightly lower recall
values.</p>
        <p>On manual inspection, we identified that the SciBERT and
CNN models do not work when only a single sentence is
given but critical information about an entity from the
preceding or succeeding sentence is needed for the decision. For
instance, in the following excerpt, the usage of the method
is not recognized if only the second sentence is given to the
models: “In this paper, we introduce Invariant Information
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        <p>ANN
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        <p>ANN
CNN
SVM
PCA
80
30 2005 2007 2009 2011 2013 2015 2017 2018
(a) Usage of selected machine learning (b) Usage of selected machine learning meth- (c) Usage of machine learning data sets over
methods over time relative to total mentions ods over time relative to all computer vision time.
in papers. papers.</p>
        <p>Clustering (IIC), a method that [...]. IIC is a generic
clustering algorithm that directly trains [...].”</p>
        <p>Furthermore, it can be seen that pronouns, such as “we,”
give the models a strong hint that an entity has been used.</p>
        <p>However, in some cases, such as mathematical notations,
this may lead to a false positive classification: “We can write
the joint update for all as Restrict the update to define a
contraction mapping in the Euclidean metric.”
Generalization across Entity Types. We also evaluate
how well the usage classification models generalize to other
entity types. For this purpose, we apply all models trained on
the METHOD entity type to DATASETS. All examined
models perform slightly worse regarding the F1 score, but still
achieve very high recall values. This suggests that sentences
in which methods are proposed or described do not
differ too much from sentences that contain information about
datasets. Out of all tested models, the SciBERT model
generalizes the best to another entity type.</p>
        <p>Further Studies. We also study whether information
about the current section improves the performance of our
classification models. Thus, we prepend the title of the
current section to the input sentence and retrain all
models. Our results show negligible performance improvements
from this modification.</p>
        <p>
          Finally, we investigate the extent to which our created data
set differs from the SciREX data set
          <xref ref-type="bibr" rid="ref5">(Jain et al. 2020)</xref>
          containing salient information of publications. Specifically, we
study the degree to which our definition of used entities
differs from salient entities considered by Jain et al. Salient
entities are defined as necessary to describe the results of a
paper and thus are semantically similar to our definition of
used entities. We find for our method annotation set that only
12 out of 1,000 entries are labeled as salient in the original
paper, which results in an MCC of 0.027 with our labels.
        </p>
        <p>For datasets, 39 entries are labeled as salient with an MCC
of 0.011. In comparison, our created annotation data
contains roughly similar amounts of used and non-used (e.g.,
proposed, only mentioned) entities, which allows us to
extract and analyze considerably more used entities than we
can with the saliency approach.
4.3</p>
      </sec>
      <sec id="sec-4-4">
        <title>Application</title>
        <p>
          We apply our framework to a corpus of 25,060 full-text
machine learning papers from the MAG
          <xref ref-type="bibr" rid="ref16">(Sinha et al. 2015)</xref>
          combined with unpaywall. The publication dates range from
2005 to 2018 and for each year we draw the same number
of papers to compare relative usages. We process the
publications using GROBID
          <xref ref-type="bibr" rid="ref9">(Lopez 2009)</xref>
          to extract the full text
as well as the title and all section names. We extract 438,707
method and 98,276 dataset entities from our corpus. Out of
all extracted entities, 56% are classified as used concerning
the methods and 68% concerning the datasets.
        </p>
        <p>Analyzing Relative Usage We first study how many
publications used specific entities compared to the number of
publications in which the same entities were only
mentioned. This relative measurement allows us to perform a
more granular trend analysis because irrelevant entities that
are never actually used will not be over-represented in the
results.</p>
        <p>Figure 4a shows this relative usage for selected machine
learning methods over time. The usage of artificial neural
networks (ANNs) and support vector machines (SVMs) is
mostly constant between 60 and 75 % for all papers that
mention one or the other term, but a slight downward trend
is discernible for plain ANNs. The relative usage of the
principal component analysis (PCA) shows a higher variability
due to fewer absolute mentions but is used up to 75 % of the
time if it is mentioned. For convolutional neural networks
(CNNs), we only show values from 2012 and later because
only a few mentions of CNNs occur in earlier years. Still,
a clear trend is visible, where at the beginning in 2012 only
around 35 % of papers that mentioned CNNs also used them
for their work, whereas in 2018 the value was greater than
55 %.</p>
        <p>Analyzing Specific Domains For another data study, we
leverage the knowledge of the MAKG to select only
publications from a specific computer science domain and analyze
this subset of publications over time. Figure 4b shows the
usage of selected machine learning methods in the computer
vision field, which is one of the most popular categories by
number of papers in our set. Here, we only analyze the
relative number of publications in which an entity has been used,
instead of the number of named entity occurrences. Until
2015, the most used methods were ANNs and SVMs, which
together have been used in around 30% of all computer
vision papers. Since 2014, the usage of CNNs has steadily
grown and is now the most used computer vision method.
In turn, the number of papers that use SVMs and PCA has
rather declined. Compared with Figure 4a, it can be seen that
the relative usage of CNNs has increased since 2016. All this
demonstrates that such a study would not be possible
without an approach as proposed in this paper, which determines
the actual usage of mentioned entities.</p>
        <p>We also apply our classification pipeline to DATASET
entities. Figure 4c shows the absolute amount of publications
for the top four extracted datasets. A clear trend is visible
for image recognition data sets, such as MNIST and
ImageNet, which also correlates with the usage of CNNs in the
computer vision domain. This again confirms the rising
popularity of the specific domain. Another trend is visible for
Wikipedia, which has become popular in research on
knowledge representation and natural language processing.
5</p>
      </sec>
    </sec>
    <sec id="sec-5">
      <title>Data Provisioning</title>
      <p>We apply our framework to all computer science papers
given both in the MAG and unpaywall (510,027 papers).
Overall, we obtained 771,000 mentions of used methods and
449,000 mentions of used datasets. We provide the dataset
online for further use (see our repository).</p>
      <p>6</p>
    </sec>
    <sec id="sec-6">
      <title>Conclusion</title>
      <p>In this paper, we proposed an approach to identifying
methods and datasets in texts that have actually been used by the
authors. Our approach first recognizes datasets and
methods in the text by means of a domain-specific named entity
recognition with minimal human interaction. It then
classifies these mentions into used vs. non-used. The obtained
labels are aggregated on the document level and integrated
into the Microsoft Academic Knowledge Graph modeling
publications’ metadata. In experiments based on the
Microsoft Academic Graph, we showed that both method and
dataset mentions can be identified and correctly classified
with respect to their usage. Our approach, as well as our
dataset containing the usage information of methods and
datasets mentioned in 510,000 papers, can be used for
research impact quantification tasks and further studies in the
area of digital libraries.</p>
      <p>In the future, we plan to use our framework with respect
to other entity types, such as task and evaluation metric.
Finally, a promising idea is to build a recommender system for
scientific publications using our framework.</p>
    </sec>
  </body>
  <back>
    <ref-list>
      <ref id="ref1">
        <mixed-citation>
          <string-name>
            <surname>Beltagy</surname>
            ,
            <given-names>I.</given-names>
          </string-name>
          ; Lo,
          <string-name>
            <given-names>K.</given-names>
            ; and
            <surname>Cohan</surname>
          </string-name>
          ,
          <string-name>
            <surname>A.</surname>
          </string-name>
          <year>2019</year>
          .
          <article-title>SciBERT: A Pretrained Language Model for Scientific Text</article-title>
          . In Inui, K.;
          <string-name>
            <surname>Jiang</surname>
            ,
            <given-names>J.</given-names>
          </string-name>
          ;
          <string-name>
            <surname>Ng</surname>
            ,
            <given-names>V.</given-names>
          </string-name>
          ; and
          <string-name>
            <surname>Wan</surname>
          </string-name>
          , X., eds.,
          <source>Proceedings of the 2019 Conference on Empirical Methods in Natural Language Processing and the 9th International Joint Conference on Natural Language Processing</source>
          , EMNLP-IJCNLP'
          <volume>19</volume>
          ,
          <fpage>3613</fpage>
          -
          <lpage>3618</lpage>
          .
        </mixed-citation>
      </ref>
      <ref id="ref2">
        <mixed-citation>
          <string-name>
            <surname>Fa</surname>
            ¨rber,
            <given-names>M.</given-names>
          </string-name>
          <year>2019</year>
          .
          <article-title>The Microsoft Academic Knowledge Graph: A Linked Data Source with 8 Billion Triples of Scholarly Data</article-title>
          .
          <source>In Proceedings of the International Semantic Web Conference</source>
          , ISWC'
          <volume>19</volume>
          ,
          <fpage>113</fpage>
          -
          <lpage>129</lpage>
          .
        </mixed-citation>
      </ref>
      <ref id="ref3">
        <mixed-citation>
          <string-name>
            <surname>Ga</surname>
          </string-name>
          ´bor, K.;
          <string-name>
            <surname>Buscaldi</surname>
            ,
            <given-names>D.</given-names>
          </string-name>
          ;
          <string-name>
            <surname>Schumann</surname>
            ,
            <given-names>A.</given-names>
          </string-name>
          ; QasemiZadeh,
          <string-name>
            <given-names>B.</given-names>
            ;
            <surname>Zargayouna</surname>
          </string-name>
          , H.; and Charnois,
          <string-name>
            <surname>T.</surname>
          </string-name>
          <year>2018</year>
          . SemEval
          <article-title>-2018 Task 7: Semantic Relation Extraction and Classification in Scientific Papers</article-title>
          .
          <source>In Proceedings of The 12th International Workshop on Semantic Evaluation</source>
          , SemEval@NAACL-HLT'
          <volume>18</volume>
          ,
          <fpage>679</fpage>
          -
          <lpage>688</lpage>
          .
        </mixed-citation>
      </ref>
      <ref id="ref4">
        <mixed-citation>
          <string-name>
            <surname>Gupta</surname>
            ,
            <given-names>S.</given-names>
          </string-name>
          ; and
          <string-name>
            <surname>Manning</surname>
            ,
            <given-names>C. D.</given-names>
          </string-name>
          <year>2011</year>
          .
          <article-title>Analyzing the Dynamics of Research by Extracting Key Aspects of Scientific Papers</article-title>
          .
          <source>In Proceedings of the 5th International Joint Conference on Natural Language Processing</source>
          , IJCNLP'
          <volume>11</volume>
          ,
          <fpage>1</fpage>
          -
          <lpage>9</lpage>
          .
        </mixed-citation>
      </ref>
      <ref id="ref5">
        <mixed-citation>
          <string-name>
            <surname>Jain</surname>
            , S.; van Zuylen,
            <given-names>M.</given-names>
          </string-name>
          ;
          <string-name>
            <surname>Hajishirzi</surname>
          </string-name>
          , H.; and
          <string-name>
            <surname>Beltagy</surname>
            ,
            <given-names>I.</given-names>
          </string-name>
          <year>2020</year>
          .
        </mixed-citation>
      </ref>
      <ref id="ref6">
        <mixed-citation>
          <article-title>SciREX: A Challenge Dataset for Document-Level Information Extraction</article-title>
          .
          <source>In Proceedings of the 58th Annual Meeting of the Association for Computational Linguistics</source>
          , ACL'
          <volume>20</volume>
          ,
          <fpage>7506</fpage>
          -
          <lpage>7516</lpage>
          .
        </mixed-citation>
      </ref>
      <ref id="ref7">
        <mixed-citation>
          <string-name>
            <surname>Kim</surname>
            ,
            <given-names>Y.</given-names>
          </string-name>
          <year>2014</year>
          .
          <article-title>Convolutional Neural Networks for Sentence Classification</article-title>
          . In
          <string-name>
            <surname>Moschitti</surname>
          </string-name>
          , A.;
          <string-name>
            <surname>Pang</surname>
            ,
            <given-names>B.</given-names>
          </string-name>
          ; and
          <string-name>
            <surname>Daelemans</surname>
          </string-name>
          , W., eds.,
          <source>Proceedings of the 2014 Conference on Empirical Methods in Natural Language Processing</source>
          , EMNLP'
          <volume>14</volume>
          ,
          <fpage>1746</fpage>
          -
          <lpage>1751</lpage>
          .
        </mixed-citation>
      </ref>
      <ref id="ref8">
        <mixed-citation>
          <string-name>
            <surname>Lample</surname>
            ,
            <given-names>G.</given-names>
          </string-name>
          ; Ballesteros,
          <string-name>
            <given-names>M.</given-names>
            ;
            <surname>Subramanian</surname>
          </string-name>
          ,
          <string-name>
            <given-names>S.</given-names>
            ;
            <surname>Kawakami</surname>
          </string-name>
          ,
          <string-name>
            <given-names>K.</given-names>
            ; and
            <surname>Dyer</surname>
          </string-name>
          ,
          <string-name>
            <surname>C.</surname>
          </string-name>
          <year>2016</year>
          .
          <article-title>Neural Architectures for Named Entity Recognition</article-title>
          .
          <source>In Proceedings of the</source>
          <year>2016</year>
          <article-title>Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies</article-title>
          , NAACL-HLT'
          <volume>16</volume>
          ,
          <fpage>260</fpage>
          -
          <lpage>270</lpage>
          .
        </mixed-citation>
      </ref>
      <ref id="ref9">
        <mixed-citation>
          <string-name>
            <surname>Lopez</surname>
            ,
            <given-names>P.</given-names>
          </string-name>
          <year>2009</year>
          .
          <article-title>GROBID: Combining Automatic Bibliographic Data Recognition and Term Extraction for Scholarship Publications</article-title>
          .
          <source>In Proceedings of the 13th European Conference on Digital Libraries</source>
          , ECDL'
          <volume>09</volume>
          ,
          <fpage>473</fpage>
          -
          <lpage>474</lpage>
          .
        </mixed-citation>
      </ref>
      <ref id="ref10">
        <mixed-citation>
          <string-name>
            <surname>Luan</surname>
            ,
            <given-names>Y.</given-names>
          </string-name>
          <year>2019</year>
          .
          <article-title>Information Extraction from Scientific Literature for Method Recommendation</article-title>
          . arXiv preprint arXiv:
          <year>1901</year>
          .00401 .
        </mixed-citation>
      </ref>
      <ref id="ref11">
        <mixed-citation>
          <string-name>
            <surname>Luan</surname>
            ,
            <given-names>Y.</given-names>
          </string-name>
          ;
          <string-name>
            <surname>He</surname>
            ,
            <given-names>L.</given-names>
          </string-name>
          ;
          <string-name>
            <surname>Ostendorf</surname>
            ,
            <given-names>M.</given-names>
          </string-name>
          ; and Hajishirzi,
          <string-name>
            <surname>H.</surname>
          </string-name>
          <year>2018</year>
          .
        </mixed-citation>
      </ref>
      <ref id="ref12">
        <mixed-citation>
          <string-name>
            <surname>Multi-Task Identification</surname>
          </string-name>
          of Entities, Relations, and
          <article-title>Coreference for Scientific Knowledge Graph Construction</article-title>
          .
          <source>In Proceedings of the 2018 Conference on Empirical Methods in Natural Language Processing</source>
          , EMNLP'
          <volume>18</volume>
          ,
          <fpage>3219</fpage>
          -
          <lpage>3232</lpage>
          .
        </mixed-citation>
      </ref>
      <ref id="ref13">
        <mixed-citation>
          <string-name>
            <surname>Ma</surname>
            ,
            <given-names>X.</given-names>
          </string-name>
          ; and
          <string-name>
            <surname>Hovy</surname>
            ,
            <given-names>E. H.</given-names>
          </string-name>
          <year>2016</year>
          .
          <article-title>End-to-end Sequence Labeling via Bi-directional LSTM-CNNs-CRF</article-title>
          .
          <article-title>In Proceedings of the 54th Annual Meeting of the Association for Computational Linguistics</article-title>
          , ACL'
          <fpage>16</fpage>
          .
        </mixed-citation>
      </ref>
      <ref id="ref14">
        <mixed-citation>
          <string-name>
            <surname>Mesbah</surname>
            ,
            <given-names>S.</given-names>
          </string-name>
          ;
          <string-name>
            <surname>Lofi</surname>
            ,
            <given-names>C.</given-names>
          </string-name>
          ;
          <string-name>
            <surname>Torre</surname>
            ,
            <given-names>M. V.</given-names>
          </string-name>
          ;
          <string-name>
            <surname>Bozzon</surname>
            ,
            <given-names>A.</given-names>
          </string-name>
          ; and Houben,
          <string-name>
            <surname>G.</surname>
          </string-name>
          <year>2018</year>
          .
          <article-title>TSE-NER: An Iterative Approach for Long-Tail Entity Extraction in Scientific Publications</article-title>
          .
          <source>In Proceedings of the International Semantic Web Conference</source>
          , ISWC'
          <volume>18</volume>
          ,
          <fpage>127</fpage>
          -
          <lpage>143</lpage>
          .
        </mixed-citation>
      </ref>
      <ref id="ref15">
        <mixed-citation>
          2017.
          <article-title>Automatically Extracting Action Graphs from Materials Science Synthesis Procedures</article-title>
          .
          <source>CoRR abs/1711</source>
          .06872.
        </mixed-citation>
      </ref>
      <ref id="ref16">
        <mixed-citation>
          <string-name>
            <surname>Sinha</surname>
            ,
            <given-names>A.</given-names>
          </string-name>
          ;
          <string-name>
            <surname>Shen</surname>
            ,
            <given-names>Z.</given-names>
          </string-name>
          ;
          <string-name>
            <surname>Song</surname>
            ,
            <given-names>Y.</given-names>
          </string-name>
          ; Ma, H.;
          <string-name>
            <surname>Eide</surname>
            ,
            <given-names>D.</given-names>
          </string-name>
          ;
          <string-name>
            <surname>Hsu</surname>
            ,
            <given-names>B.-J. P.</given-names>
          </string-name>
          ; and
          <string-name>
            <surname>Wang</surname>
            ,
            <given-names>K.</given-names>
          </string-name>
          <year>2015</year>
          .
          <article-title>An Overview of Microsoft Academic Service (MAS) and Applications</article-title>
          .
          <source>In Proceedings of 24th International Conference on World Wide Web Companion</source>
          , WWW'
          <volume>15</volume>
          ,
          <fpage>243</fpage>
          -
          <lpage>246</lpage>
          .
        </mixed-citation>
      </ref>
      <ref id="ref17">
        <mixed-citation>
          <string-name>
            <surname>Tchoua</surname>
            ,
            <given-names>R.</given-names>
          </string-name>
          ;
          <string-name>
            <surname>Ajith</surname>
            ,
            <given-names>A.</given-names>
          </string-name>
          ;
          <string-name>
            <surname>Hong</surname>
            ,
            <given-names>Z.</given-names>
          </string-name>
          ;
          <string-name>
            <surname>Ward</surname>
            ,
            <given-names>L.</given-names>
          </string-name>
          ;
          <string-name>
            <surname>Chard</surname>
            ,
            <given-names>K.</given-names>
          </string-name>
          ;
          <string-name>
            <surname>Audus</surname>
            ,
            <given-names>D.</given-names>
          </string-name>
          ;
          <string-name>
            <surname>Patel</surname>
          </string-name>
          , S.; de Pablo, J.; and
          <string-name>
            <surname>Foster</surname>
            ,
            <given-names>I.</given-names>
          </string-name>
          <year>2019</year>
          .
          <article-title>Active Learning Yields Better Training Data for Scientific Named Entity Recognition</article-title>
          .
          <source>In Proceedings of the 15th International Conference on eScience, eScience'19</source>
          ,
          <fpage>126</fpage>
          -
          <lpage>135</lpage>
          .
        </mixed-citation>
      </ref>
      <ref id="ref18">
        <mixed-citation>
          <string-name>
            <surname>Tsai</surname>
          </string-name>
          , C.-T.;
          <string-name>
            <surname>Kundu</surname>
          </string-name>
          , G.; and
          <string-name>
            <surname>Roth</surname>
            ,
            <given-names>D.</given-names>
          </string-name>
          <year>2013</year>
          .
          <article-title>Concept-Based Analysis of Scientific Literature</article-title>
          .
          <source>In Proceedings of the 22nd ACM International Conference on Information and Knowledge Management</source>
          , CIKM'
          <volume>13</volume>
          ,
          <fpage>1733</fpage>
          -
          <lpage>1738</lpage>
          .
        </mixed-citation>
      </ref>
      <ref id="ref19">
        <mixed-citation>
          <string-name>
            <surname>Vliegenthart</surname>
            ,
            <given-names>D.</given-names>
          </string-name>
          ;
          <string-name>
            <surname>Mesbah</surname>
            ,
            <given-names>S.</given-names>
          </string-name>
          ;
          <string-name>
            <surname>Lofi</surname>
            ,
            <given-names>C.</given-names>
          </string-name>
          ;
          <string-name>
            <surname>Aizawa</surname>
            ,
            <given-names>A.</given-names>
          </string-name>
          ; and
          <string-name>
            <surname>Bozzon</surname>
            ,
            <given-names>A.</given-names>
          </string-name>
          <year>2019</year>
          .
          <article-title>Coner: A Collaborative Approach for LongTail Named Entity Recognition in Scientific Publications</article-title>
          .
          <source>In Proceedings of the 23rd International Conference on Theory and Practice of Digital Libraries, TPDL'19</source>
          ,
          <fpage>3</fpage>
          -
          <lpage>17</lpage>
          .
        </mixed-citation>
      </ref>
    </ref-list>
  </back>
</article>